VVP-pub

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gnomAD vvp non-existant + vcf gives segmentation error

2

Since there is no gnomAD vvp build anymore I tried to run the example build (which works in the example provided), it gives segmentation error in my own vcf file...

Bradshard

how to generate percentile scores

1

Hi I have successfully run vvp on my vcf file, but the output does not contain percentile scores. How do I compile percentile scores for my gene of interest using...

odettelegrange

Now，I get CSQ through `vep`, like this:  But when i run the shell ``` ../VVP -i gnomad_chr_1_1000.vcf.gz -d gnomad.062717.build -v CSQ,4,6,1,15 1> target.spiked.vvp.out ``` The output `target.spiked.vvp.out` has nothing:...

lqr131115

WARNING: chromosome not in offsets

1

Hi Steven, I tried running vvp on a test sample data and but it gives 'WARNING: chromosome chrY not in offsets' error all chr, also I have not been able...

sandeepyuva1994

how to use background based on gnomAD ?

7

hi I I've successfully run the VVP,but I do know how to use background based on gnomAD? I download gnomad.062717.build.tar.gz and unzip it ，can not find gnomad.062717.build.bin and gnomad.062717.build.max. can...

hsxsin

Hi, I am having trouble creating a background using gnomAD v3. https://storage.googleapis.com/gnomad-public/release/3.0/vcf/genomes/gnomad.genomes.r3.0.sites.vcf.bgz Command ran: `build_background -i gnomad.genomes.r3.0.sites.vcf.bgz -b 1 -v CSQ,4,6,1,15 -o test.out ` I receive the error: ``` #chr...

j2moreno

When two or more VVP processes are run concurrently they may all need to open the same background for memory mapping. For some reason the background is opened for read...

ink1

request: bioconda

1

Hi Great tool - any chance you can or will get this up as a package in bioconda? Would be great for the bioinformatics and NGS community Best Steve

snewhouse

how to interpret output file

1

Hi, I've successfully run the VVP and got the output result (Hooray!), just wondered how should I interpret the output file, and what does each column mean in the output?...

hurleyLi